Performance Optimization Strategies for Transactional Memory Applications

This thesis presents tools for Transactional Memory (TM) applications that cover multiple TM systems (Software, Hardware, and hybrid TM) and use information of all different layers of the TM software stack. Therefore, this thesis addresses a number of challenges to extract static information, information about the run time behavior, and expert-level knowledge to develop these new methods and strategies for the optimization of TM applications

Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions

Infrastructure for Performance Monitoring and Analysis of Systems and Applications

The growth of High Performance Computer (HPC) systems increases the complexity with respect to understanding resource utilization, system management, and performance issues. HPC performance monitoring tools need to collect information at both the application and system levels to yield a complete performance picture. Existing approaches limit the abilities of the users to do meaningful analysis on actionable timescale. Efficient infrastructures are required to support largescale systems performance data analysis for both run-time troubleshooting and post-run processing modes. In this dissertation, we present methods to fill these gaps in the infrastructure for HPC performance monitoring and analysis. First, we enhance the architecture of a monitoring system to integrate streaming analysis capabilities at arbitrary locations within its data collection, transport, and aggregation facilities. Next, we present an approach to streaming collection of application performance data. We integrate these methods with a monitoring system used on large-scale computational platforms. Finally, we present a new approach for constructing durable transactional linked data structures that takes advantage of byte-addressable non-volatile memory technologies. Transactional data structures are building blocks of in-memory databases that are used by HPC monitoring systems to store and retrieve data efficiently. We evaluate the presented approaches on a series of case studies. The experiment results demonstrate the impact of our tools, while keeping the overhead in an acceptable margin

Storage Solutions for Big Data Systems: A Qualitative Study and Comparison

Big data systems development is full of challenges in view of the variety of application areas and domains that this technology promises to serve. Typically, fundamental design decisions involved in big data systems design include choosing appropriate storage and computing infrastructures. In this age of heterogeneous systems that integrate different technologies for optimized solution to a specific real world problem, big data system are not an exception to any such rule. As far as the storage aspect of any big data system is concerned, the primary facet in this regard is a storage infrastructure and NoSQL seems to be the right technology that fulfills its requirements. However, every big data application has variable data characteristics and thus, the corresponding data fits into a different data model. This paper presents feature and use case analysis and comparison of the four main data models namely document oriented, key value, graph and wide column. Moreover, a feature analysis of 80 NoSQL solutions has been provided, elaborating on the criteria and points that a developer must consider while making a possible choice. Typically, big data storage needs to communicate with the execution engine and other processing and visualization technologies to create a comprehensive solution. This brings forth second facet of big data storage, big data file formats, into picture. The second half of the research paper compares the advantages, shortcomings and possible use cases of available big data file formats for Hadoop, which is the foundation for most big data computing technologies. Decentralized storage and blockchain are seen as the next generation of big data storage and its challenges and future prospects have also been discussed

A framework for multidimensional indexes on distributed and highly-available data stores

Spatial Big Data is considered an essential trend in future scientific and business applications. Indeed, research instruments, medical devices, and social networks generate hundreds of peta bytes of spatial data per year. However, as many authors have pointed out, the lack of specialized frameworks dealing with such kind of data is limiting possible applications and probably precluding many scientific breakthroughs. In this thesis, we describe three HPC scientific applications, ranging from molecular dynamics, neuroscience analysis, and physics simulations, where we experience first hand the limits of the existing technologies. Thanks to our experience, we define the desirable missing functionalities, and we focus on two features that when combined significantly improve the way scientific data is analyzed. On one side, scientific simulations generate complex datasets where multiple correlated characteristics describe each item. For instance, a particle might have a space position (x,y,z) at a given time (t). If we want to find all elements within the same area and period, we either have to scan the whole dataset, or we must organize the data so that all items in the same space and time are stored together. The second approach is called Multidimensional Indexing (MI), and it uses different techniques to cluster and to organize similar data together. On the other side, approximate analytics has been often indicated as a smart and flexible way to explore large datasets in a short period. Approximate analytics includes a broad family of algorithms which aims to speed up analytical workloads by relaxing the precision of the results within a specific interval of confidence. For instance, if we want to know the average age in a group with 1-year precision, we can consider just a random fraction of all the people, thus reducing the amount of calculation. But if we also want less I/O operations, we need efficient data sampling, which means organizing data in a way that we do not need to scan the whole data set to generate a random sample of it. According to our analysis, combining Multidimensional Indexing with efficient data Sampling (MIS) is a vital missing feature not available in the current distributed data management solutions. This thesis aims to solve such a shortcoming and it provides novel scalable solutions. At first, we describe the existing data management alternatives; then we motivate our preference for NoSQL key-value databases. Secondly, we propose an analytical model to study the influence of data models on the scalability and performance of this kind of distributed database. Thirdly, we use the analytical model to design two novel multidimensional indexes with efficient data sampling: the D8tree and the AOTree. Our first solution, the D8tree, improves state of the art for approximate spatial queries on static and mostly read dataset. Later, we enhanced the data ingestion capability or our approach by introducing the AOTree, an algorithm that enables the query performance of the D8tree even for HPC write-intensive applications. We compared our solution with PostgreSQL and plain storage, and we demonstrate that our proposal has better performance and scalability. Finally, we describe Qbeast, the novel distributed system that implements the D8tree and the AOTree using NoSQL technologies, and we illustrate how Qbeast simplifies the workflow of scientists in various HPC applications providing a scalable and integrated solution for data analysis and management.La gestión de BigData con información espacial está considerada como una tendencia esencial en el futuro de las aplicaciones científicas y de negocio. De hecho, se generan cientos de petabytes de datos espaciales por año mediante instrumentos de investigación, dispositivos médicos y redes sociales. Sin embargo, tal y como muchos autores han señalado, la falta de entornos especializados en manejar este tipo de datos está limitando sus posibles aplicaciones y está impidiendo muchos avances científicos. En esta tesis, describimos 3 aplicaciones científicas HPC, que cubren los ámbitos de dinámica molecular, análisis neurocientífico y simulaciones físicas, donde hemos experimentado en primera mano las limitaciones de las tecnologías existentes. Gracias a nuestras experiencias, hemos podido definir qué funcionalidades serían deseables y no existen, y nos hemos centrado en dos características que, al combinarlas, mejoran significativamente la manera en la que se analizan los datos científicos. Por un lado, las simulaciones científicas generan conjuntos de datos complejos, en los que cada elemento es descrito por múltiples características correlacionadas. Por ejemplo, una partícula puede tener una posición espacial (x, y, z) en un momento dado (t). Si queremos encontrar todos los elementos dentro de la misma área y periodo, o bien recorremos y analizamos todo el conjunto de datos, o bien organizamos los datos de manera que se almacenen juntos todos los elementos que comparten área en un momento dado. Esta segunda opción se conoce como Indexación Multidimensional (IM) y usa diferentes técnicas para agrupar y organizar datos similares. Por otro lado, se suele señalar que las analíticas aproximadas son una manera inteligente y flexible de explorar grandes conjuntos de datos en poco tiempo. Este tipo de analíticas incluyen una amplia familia de algoritmos que acelera el tiempo de procesado, relajando la precisión de los resultados dentro de un determinado intervalo de confianza. Por ejemplo, si queremos saber la edad media de un grupo con precisión de un año, podemos considerar sólo un subconjunto aleatorio de todas las personas, reduciendo así la cantidad de cálculo. Pero si además queremos menos operaciones de entrada/salida, necesitamos un muestreo eficiente de datos, que implica organizar los datos de manera que no necesitemos recorrerlos todos para generar una muestra aleatoria. De acuerdo con nuestros análisis, la combinación de Indexación Multidimensional con Muestreo eficiente de datos (IMM) es una característica vital que no está disponible en las soluciones actuales de gestión distribuida de datos. Esta tesis pretende resolver esta limitación y proporciona unas soluciones novedosas que son escalables. En primer lugar, describimos las alternativas de gestión de datos que existen y motivamos nuestra preferencia por las bases de datos NoSQL basadas en clave-valor. En segundo lugar, proponemos un modelo analítico para estudiar la influencia que tienen los modelos de datos sobre la escalabilidad y el rendimiento de este tipo de bases de datos distribuidas. En tercer lugar, usamos el modelo analítico para diseñar dos novedosos algoritmos IMM: el D8tree y el AOTree. Nuestra primera solución, el D8tree, mejora el estado del arte actual para consultas espaciales aproximadas, cuando el conjunto de datos es estático y mayoritariamente de lectura. Después, mejoramos la capacidad de ingestión introduciendo el AOTree, un algoritmo que conserva el rendimiento del D8tree incluso para aplicaciones HPC intensivas en escritura. Hemos comparado nuestra solución con PostgreSQL y almacenamiento plano demostrando que nuestra propuesta mejora tanto el rendimiento como la escalabilidad. Finalmente, describimos Qbeast, el sistema que implementa los algoritmos D8tree y AOTree, e ilustramos cómo Qbeast simplifica el flujo de trabajo de los científicos ofreciendo una solución escalable e integraPostprint (published version

A new approach to reversible computing with applications to speculative parallel simulation

In this thesis, we propose an innovative approach to reversible computing that shifts the focus from the operations to the memory outcome of a generic program. This choice allows us to overcome some typical challenges of "plain" reversible computing. Our methodology is to instrument a generic application with the help of an instrumentation tool, namely Hijacker, which we have redesigned and developed for the purpose. Through compile-time instrumentation, we enhance the program's code to keep track of the memory trace it produces until the end. Regardless of the complexity behind the generation of each computational step of the program, we can build inverse machine instructions just by inspecting the instruction that is attempting to write some value to memory. Therefore from this information, we craft an ad-hoc instruction that conveys this old value and the knowledge of where to replace it. This instruction will become part of a more comprehensive structure, namely the reverse window. Through this structure, we have sufficient information to cancel all the updates done by the generic program during its execution. In this writing, we will discuss the structure of the reverse window, as the building block for the whole reversing framework we designed and finally realized. Albeit we settle our solution in the specific context of the parallel discrete event simulation (PDES) adopting the Time Warp synchronization protocol, this framework paves the way for further general-purpose development and employment. We also present two additional innovative contributions coming from our innovative reversibility approach, both of them still embrace traditional state saving-based rollback strategy. The first contribution aims to harness the advantages of both the possible approaches. We implement the rollback operation combining state saving together with our reversible support through a mathematical model. This model enables the system to choose in autonomicity the best rollback strategy, by the mutable runtime dynamics of programs. The second contribution explores an orthogonal direction, still related to reversible computing aspects. In particular, we will address the problem of reversing shared libraries. Indeed, leading from their nature, shared objects are visible to the whole system and so does every possible external modification of their code. As a consequence, it is not possible to instrument them without affecting other unaware applications. We propose a different method to deal with the instrumentation of shared objects. All our innovative proposals have been assessed using the last generation of the open source ROOT-Sim PDES platform, where we integrated our solutions. ROOT-Sim is a C-based package implementing a general purpose simulation environment based on the Time Warp synchronization protocol

Análise de malware com suporte de hardware

Orientadores: Paulo Lício de Geus, André Ricardo Abed GrégioDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: O mundo atual é impulsionado pelo uso de sistemas computacionais, estando estes pre- sentes em todos aspectos da vida cotidiana. Portanto, o correto funcionamento destes é essencial para se assegurar a manutenção das possibilidades trazidas pelos desenvolvi- mentos tecnológicos. Contudo, garantir o correto funcionamento destes não é uma tarefa fácil, dado que indivíduos mal-intencionados tentam constantemente subvertê-los visando benefíciar a si próprios ou a terceiros. Os tipos mais comuns de subversão são os ataques por códigos maliciosos (malware), capazes de dar a um atacante controle total sobre uma máquina. O combate à ameaça trazida por malware baseia-se na análise dos artefatos coletados de forma a permitir resposta aos incidentes ocorridos e o desenvolvimento de contramedidas futuras. No entanto, atacantes têm se especializado em burlar sistemas de análise e assim manter suas operações ativas. Para este propósito, faz-se uso de uma série de técnicas denominadas de "anti-análise", capazes de impedir a inspeção direta dos códigos maliciosos. Dentre essas técnicas, destaca-se a evasão do processo de análise, na qual são empregadas exemplares capazes de detectar a presença de um sistema de análise para então esconder seu comportamento malicioso. Exemplares evasivos têm sido cada vez mais utilizados em ataques e seu impacto sobre a segurança de sistemas é considerá- vel, dado que análises antes feitas de forma automática passaram a exigir a supervisão de analistas humanos em busca de sinais de evasão, aumentando assim o custo de se manter um sistema protegido. As formas mais comuns de detecção de um ambiente de análise se dão através da detecção de: (i) código injetado, usado pelo analista para inspecionar a aplicação; (ii) máquinas virtuais, usadas em ambientes de análise por questões de escala; (iii) efeitos colaterais de execução, geralmente causados por emuladores, também usados por analistas. Para lidar com malware evasivo, analistas tem se valido de técnicas ditas transparentes, isto é, que não requerem injeção de código nem causam efeitos colaterais de execução. Um modo de se obter transparência em um processo de análise é contar com suporte do hardware. Desta forma, este trabalho versa sobre a aplicação do suporte de hardware para fins de análise de ameaças evasivas. No decorrer deste texto, apresenta-se uma avaliação das tecnologias existentes de suporte de hardware, dentre as quais máqui- nas virtuais de hardware, suporte de BIOS e monitores de performance. A avaliação crítica de tais tecnologias oferece uma base de comparação entre diferentes casos de uso. Além disso, são enumeradas lacunas de desenvolvimento existentes atualmente. Mais que isso, uma destas lacunas é preenchida neste trabalho pela proposição da expansão do uso dos monitores de performance para fins de monitoração de malware. Mais especificamente, é proposto o uso do monitor BTS para fins de construção de um tracer e um debugger. O framework proposto e desenvolvido neste trabalho é capaz, ainda, de lidar com ataques do tipo ROP, um dos mais utilizados atualmente para exploração de vulnerabilidades. A avaliação da solução demonstra que não há a introdução de efeitos colaterais, o que per- mite análises de forma transparente. Beneficiando-se desta característica, demonstramos a análise de aplicações protegidas e a identificação de técnicas de evasãoAbstract: Today¿s world is driven by the usage of computer systems, which are present in all aspects of everyday life. Therefore, the correct working of these systems is essential to ensure the maintenance of the possibilities brought about by technological developments. However, ensuring the correct working of such systems is not an easy task, as many people attempt to subvert systems working for their own benefit. The most common kind of subversion against computer systems are malware attacks, which can make an attacker to gain com- plete machine control. The fight against this kind of threat is based on analysis procedures of the collected malicious artifacts, allowing the incident response and the development of future countermeasures. However, attackers have specialized in circumventing analysis systems and thus keeping their operations active. For this purpose, they employ a series of techniques called anti-analysis, able to prevent the inspection of their malicious codes. Among these techniques, I highlight the analysis procedure evasion, that is, the usage of samples able to detect the presence of an analysis solution and then hide their malicious behavior. Evasive examples have become popular, and their impact on systems security is considerable, since automatic analysis now requires human supervision in order to find evasion signs, which significantly raises the cost of maintaining a protected system. The most common ways for detecting an analysis environment are: i) Injected code detec- tion, since injection is used by analysts to inspect applications on their way; ii) Virtual machine detection, since they are used in analysis environments due to scalability issues; iii) Execution side effects detection, usually caused by emulators, also used by analysts. To handle evasive malware, analysts have relied on the so-called transparent techniques, that is, those which do not require code injection nor cause execution side effects. A way to achieve transparency in an analysis process is to rely on hardware support. In this way, this work covers the application of the hardware support for the evasive threats analysis purpose. In the course of this text, I present an assessment of existing hardware support technologies, including hardware virtual machines, BIOS support, performance monitors and PCI cards. My critical evaluation of such technologies provides basis for comparing different usage cases. In addition, I pinpoint development gaps that currently exists. More than that, I fill one of these gaps by proposing to expand the usage of performance monitors for malware monitoring purposes. More specifically, I propose the usage of the BTS monitor for the purpose of developing a tracer and a debugger. The proposed framework is also able of dealing with ROP attacks, one of the most common used technique for remote vulnerability exploitation. The framework evaluation shows no side-effect is introduced, thus allowing transparent analysis. Making use of this capability, I demonstrate how protected applications can be inspected and how evasion techniques can be identifiedMestradoCiência da ComputaçãoMestre em Ciência da ComputaçãoCAPE

Customer-Centric Sales Forecasting Model: RFM-ARIMA Approach

Background: Decision makers use the process of determining the best course of action by processing, analysing & interpreting the data to gain insights, known as Business Intelligence. Some decision support systems use sales figures to predict future expansion, but few consider the effect of customer data. Objectives: The main objective of this study is to build a model that will give a forecast based on fine-tuned sales numbers using some customer-centric features. Methods/Approach: We first use the RFM model to segment the customers into distinct segments based on customer buying characteristics and then discard the segments that are irrelevant to the business. Then we use the ARIMA model to do the sales forecasting for the remainder of the data. Results: Using this model, we were able to achieve a better fitment of the data for the prediction model and achieved a better accuracy when used after RFM analysis. Conclusions: We tried to merge two different concepts to do a cross-functional analysis for better decision-making. We were able to present the RFM-ARIMA model as a better metric or approach to fine-tune the sales analysis

Supporting Project Comprehension with Revision Control System Repository Analysis

Context: Project comprehension is an activity relevant to all aspects of software engineering, from requirements specification to maintenance. The historical, transactional data stored in revision control systems can be mined and analysed to produce a great deal of information about a project. Aims: This research aims to explore how the data-mining, analysis and presentation of revision control systems can be used to augment aspects of project comprehension, including change prediction, maintenance, visualization, management, profiling, sampling and assessment. Method: A series of case studies investigate how transactional data can be used to support project comprehension. A thematic analysis of revision logs is used to explore the development process and developer behaviour. A benchmarking study of a history-based model of change prediction is conducted to assess how successfully such a technique can be used to augment syntax-based models. A visualization tool is developed for managers of student projects with the aim of evaluating what visualizations best support their roles. Finally, a quasi-experiment is conducted to determine how well an algorithmic model can automatically select a representative sample of code entities from a project, in comparison with expert strategies. Results: The thematic analysis case study classified maintenance activities in 22 undergraduate projects and four real-world projects. The change prediction study calculated information retrieval metrics for 34 undergraduate projects and three real-world projects, as well as an in-depth exploration of the model's performance and applications in two selected projects. File samples for seven projects were generated by six experts and three heuristic models and compared to assess agreement rates, both within the experts and between the experts and the models. Conclusions: When the results from each study are evaluated together, the evidence strongly shows that the information stored in revision control systems can indeed be used to support a range of project comprehension activities in a manner which complements existing, syntax-based techniques. The case studies also help to develop the empirical foundation of repository analysis in the areas of visualization, maintenance, sampling, profiling and management; the research also shows that students can be viable substitutes for industrial practitioners in certain areas of software engineering research, which weakens one of the primary obstacles to empirical studies in these areas